20pathways ii

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1、PathwayBioinformaticsPeterD.Karp,PhDBioinformaticsResearchGroupSRIInternationalMenloPark,CApkarp@ai.sri.comBioCyc.orgOverviewDefinitionsBioCyccollectionofPathway/GenomeDatabasesAlgorithmsforpathwaybioinformaticsPathwayToolssoftwareNavigationandanalysisInfermet

2、abolicpathwaysfromgenomesPathwayToolsontologyPathwayBioinformaticsThesubfieldofbioinformaticsconcernedwithontologies,algorithms,databasesandvisualizationsofpathwaysExamples:InferenceofmetabolicpathwaysfromgenomesSchemasforpathwayDBsExchangeformatsforpathwaydat

3、aClassificationsystemsforpathwaydataPathwaydiagramlayoutalgorithmsDefinitionofMetabolicPathwaysAchemicalreactioninterconvertschemicalcompounds(analogoustoaproductionrule)A+B=C+D!Anenzymeisaproteinthataccelerateschemicalreactions.Eachenzymeisencodedbyoneormoregen

4、es.Apathwayisalinkedsetofreactions(analogoustoachainofrules)ACE!DefinitionofSmall-MoleculeMetabolismSmall-moleculemetabolismBiochemicalfactorywithinthecellHundredsofenzyme-catalyzedreactionsoperatingprincipallyonsmall-moleculesubstratesSmallMoleculeMetabolismAll

5、BiochemicalReactionsTransportSmallMoleculeMetabolismDNAReplication,BiosynthesisTranscriptionDegradationWhatisaMetabolicPathway?ApathwayisaconceptualunitofthemetabolismAnorderedsetofinterconnected,directedbiochemicalreactionsApathwayformsacoherentunit:Boundariesd

6、efinedathigh-connectivitysubstratesRegulatedasasingleunitEvolutionarilyconservedacrossorganismsasasingleunitPerformsasinglecellularfunctionHistoricallygroupedtogetherasaunitAllreactionsinasingleorganismEcoCycPathwaysBioCycCollectionof507Pathway/GenomeDatabases

7、Pathway/GenomeDatabase(PGDB)–combinesinformationaboutPathways,reactions,substratesEnzymes,transportersGenes,repliconsTranscriptionfactors/sites,promoters,operonsTier1:Literature-DerivedPGDBsMetaCycEcoCyc--EscherichiacoliK-12Tier2:Computationally-derivedDBs,S

8、omeCuration--24PGDBsHumanCycMycobacteriumtuberculosisTier3:Computationally-derivedDBs,NoCuration--481DBsFamilyofPathway/GenomeDatabases